Package picard.sam.SamErrorMetric
Class IndelErrorCalculator
- java.lang.Object
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- picard.sam.SamErrorMetric.BaseErrorCalculator
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- picard.sam.SamErrorMetric.IndelErrorCalculator
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- All Implemented Interfaces:
BaseCalculator
public class IndelErrorCalculator extends BaseErrorCalculator
A calculator that estimates the error rate of the bases it observes for indels only.
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Field Summary
Fields Modifier and Type Field Description protected long
nDeletedBases
Total number of deleted basesprotected long
nDeletions
Total number of deletionsprotected long
nInsertedBases
Total number of inserted basesprotected long
nInsertions
Total number of inserts
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Constructor Summary
Constructors Constructor Description IndelErrorCalculator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
the function by which new loci are "shown" to the calculatorIndelErrorMetric
getMetric()
Returns the metric generated by the observed lociString
getSuffix()
The suffix that pertains to the implementation of aggregation
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Method Detail
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addBase
public void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
Description copied from class:BaseErrorCalculator
the function by which new loci are "shown" to the calculator- Specified by:
addBase
in interfaceBaseCalculator
- Overrides:
addBase
in classBaseErrorCalculator
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getSuffix
public String getSuffix()
The suffix that pertains to the implementation of aggregation
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getMetric
public IndelErrorMetric getMetric()
Returns the metric generated by the observed loci
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